4D5A | pdb_00004d5a

Clostridial Cysteine protease Cwp84 C116A after propeptide cleavage


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CI7PDB ENTRY 4CI7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.18 M NACL, 90 MM TRIS PH 8.0, 18% PEG 6000, 0.02% W/V 1,4-DIAMINOBUTANE, 0.02% W/V CYSTAMINE DIHYDROCHLORIDE, 0.02% W/V DILOXANIDE FUROATE, 0.02% W/V SARCOSINE, 0.02% W/V SPERMINE, 2MM SODIUM HEPES PH 6.8
Crystal Properties
Matthews coefficientSolvent content
2.6353.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.094α = 65.22
b = 70.152β = 89.89
c = 78.852γ = 80.18
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.647.390.80.096.82.81101751
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6349.90.472.12.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4CI71.671.38104911526190.80.182520.181120.190.210550.22RANDOM15.346
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1.33-0.170.151.46-0.53-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.291
r_dihedral_angle_4_deg15.069
r_dihedral_angle_3_deg12.45
r_dihedral_angle_1_deg6.073
r_mcangle_it1.552
r_angle_refined_deg1.274
r_scbond_it1.062
r_mcbond_it0.899
r_mcbond_other0.895
r_angle_other_deg0.734
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.291
r_dihedral_angle_4_deg15.069
r_dihedral_angle_3_deg12.45
r_dihedral_angle_1_deg6.073
r_mcangle_it1.552
r_angle_refined_deg1.274
r_scbond_it1.062
r_mcbond_it0.899
r_mcbond_other0.895
r_angle_other_deg0.734
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6350
Nucleic Acid Atoms
Solvent Atoms791
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
PHASERphasing